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comparison flashlfq.xml @ 6:279fbc8ad992 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq commit a9220a40d89c0bd250002d876d4b2f751d19f3de
author galaxyp
date Thu, 25 Jan 2018 18:02:03 -0500
parents 3b0c2e1927c1
children c4c61493c9a8
comparison
equal deleted inserted replaced
5:3b0c2e1927c1 6:279fbc8ad992
1 <tool id="flashlfq" name="FlashLFQ" version="0.1.0"> 1 <tool id="flashlfq" name="FlashLFQ" version="0.1.99">
2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> 2 <description>ultrafast label-free quantification for mass-spectrometry proteomics</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.99">flashlfq</requirement> 4 <requirement type="package" version="0.1.99">flashlfq</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 #import re 7 #import re
8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv" 8 #set $idt_path = $re.sub('\s','_',$re.sub('[.][^.]*$','',$idt.display_name.split('/')[-1])) + ".psmtsv"
9 mkdir spectrum_dir; 9 ln -s '${idt}' '${idt_path}' &&
10 ln -s '${idt}' '${idt_path}'; 10 mkdir spectrum_dir &&
11 #for $peak_list in $peak_lists: 11 #for $peak_list in $peak_lists:
12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML" 12 #set $input_name = $re.sub('[.][^.]*$','',$peak_list.display_name.split('/')[-1]) + ".mzML"
13 ln -s '${peak_list}' 'spectrum_dir/${input_name}'; 13 ln -s '${peak_list}' 'spectrum_dir/${input_name}' &&
14 #end for 14 #end for
15 FlashLFQ --idt '$idt_path' --rep spectrum_dir --ppm $ppm --iso $iso --nis $nis 15
16 FlashLFQ
17 --idt '$idt_path'
18 --rep spectrum_dir
19 --ppm $ppm
20 --iso $iso
21 --nis $nis
16 #if $intensity == 'integrate': 22 #if $intensity == 'integrate':
17 --int true 23 --int true
18 #end if 24 #end if
19 #if $charge == 'precursor': 25 #if $charge == 'precursor':
20 --chg true 26 --chg true
21 #end if 27 #end if
22 $rmm $mbr 28 $rmm $mbr
23 --pau false 29 --pau false
24 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log' 30 && cat *_FlashLFQ_Log.txt | sed 's/\(Analysis summary for:\).*working./\1 /' > '$log'
25 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences' 31 && cp *_FlashLFQ_QuantifiedBaseSequences.tsv '$quantifiedBaseSequences'
88 </output> 94 </output>
89 </test> 95 </test>
90 </tests> 96 </tests>
91 <help><![CDATA[ 97 <help><![CDATA[
92 98
93 **FlashLFQ** 99 **FlashLFQ** is an ultrafast label-free quantification for mass-spectrometry proteomics.
94 100
95 **Accepted command-line arguments:** 101 **Accepted command-line arguments:**
96 102
97 :: 103 ::
98 104